Expedition to the Unknown
Long ago, before the events that lead to the loss of Al'Taieu (so over 10,000 years before present day), a group of Zilart found a Veridical Conflux allowing them to leave this dimension. What the explorers discovered beyond this conflux was the void we now know as the Threshold where the remnants of "discarded" realities were found.
The actual method of leaving this dimension isn't set in stone as a conflux, let's just say it was. It would be interesting to explore the reason behind the existence of Veridical Confuxes in this story, however I don't touch on that directly. I would not rule out the activities of Odin & Alexander (Ragnarok/Lightbringer) in this ancient time having an impact on the unrecorded history that could be used to tie in the events of ToAU.
This may have occurred at the same time that Eald'narche made a connection with the crystal, giving him the "Vision of Paradise" as the expeditionary group traveled through time, between dimensions, that sparked the interest in the rest of the Zilart to open a "gateway to paradise" somehow. The expeditionary force may or may not have not received the vision, cut off from the telepathic link shared by the Zilart when they left their home dimension. In any event, the conflux disappeared after a large group entered, never to be seen again. Some members of the expedition may have been left behind, fueling their desire to open this portal again under the misguided assumption that it was in fact a physical gateway to paradise, even though the Zilart plan to open this gateway was not really a plan to open a door, but the reunification of the mothercrystal to transform the whole universe back to a condition referred to as "paradise".
Unable to return through the conflux at first, they explored this realm. Here, they encountered an inter-dimensional traveler who taught them how to survive within Atomos' realm without being consumed by the void. The traveler had been using this "Cleft of Dimensions" for countless eons (and may have told them a tale about a world that had been split asunder when its crystals were split and then merged back together when the crystals were re-formed. This only matters if the expedition saw the same vision of the Zilart, linking the concepts of splitting & merging crystals) The exploratory group founded a new civilization within the void which began studying every alternate reality being consumed by Atomos, learning & recording that which they thought worthwhile to save from the oblivion of the void.
Watch and Learn
The immortal Zilart spent millennia learning and experiencing all there was to be seen in all the alternate realities. They accumulated a vast storehouse of knowledge that they could put to use and became masters of every style of combat they encountered, every known magic spell & every type of crafting. They used this knowledge to finally influence Atomos to open his maw to points of their choosing in both space & time, whenever they wanted. The group that managed to do this was able to exert great influence over the rest of their civilization which took on the name of that group: the Simulacrum, a name given to them by the traveler they first encountered. Being able to travel through time at their own discretion allowed them to study whatever they wished for as long as they wished, at least until Atomos got around to consuming the alternate timelines.
Passing Time
Ages passed after they had learned all they thought worth learning, thus they began to grow bored -- at this time, they turned to games for amusement. The Simulacrum took their games very seriously, especially when combat was involved. Having grown very old & complacent without anyone to truly challenge their power, the arrogance of these immortals moved them to impose arbitrary restrictions as they battled each other or on the participants in battles they watched. They began concocting powerful potions & items to influence battles as well. Their engineers also began creating artificial creatures (similar to the dolls, golems & arcana that inhabit most Zilart structures to this day,) to play new games with, test their abilities on and to challenge themselves in specific ways, known to us as the Caturae. (the Zilarts' penchant for bio-engineering monsters & weapons can be seen in Temenos and Apollyon, culminating in the creation of Ultima & Omega to battle the wyrms.)
Would You Like To Play A Game?
Of course, the biggest game of all is world domination. The only question then becomes, which world to dominate? The world most recently chosen for this "Caturariga" game was that of Abyssea. At least two players were involved. One sent game pieces into the world; including the Vorageans, hordes of powerfully enhanced beasts & the Caturae, while the other player chose heroes from the inhabitants of the world to defend it, giving them the Empyrean armor & weapons (found in other timelines), for that cause.
Clearly, the Caturae were winning (sections of the world were being destroyed in a strangely grid-like pattern, like a board game) until the adventurers from Vana'diel got involved. This may have been considered "cheating" by the opposing Caturariga player, so we may be seeing the ramifications of that scenario playing out in the invasion of the Voidwalkers - creatures that tracked the heroes down through the dimensions (we know the creators of Omega in FFXII enabled it to track Shinryu through dimensions to hunt it down & destroy it and it fits that those creators were the Zilart, since they also had a war with the Wyrms/Dragons -- imagine now if they were the same race as the Terrans from FF9... quasilumins sleeping while Garland found them a new home and bio-engineered new bodies for them -- but that's not applicable to this story at this time, just a thought)
Shinryu was set free upon Abyssea when the Abyssean versions of the Vana'diel adventurers were unable to defeat Promathia, likely due to the invasion of the Caturae (leading to the world being consumed by the emptiness.) Perhaps the Simulacrum thought it a fun goal to see if the heroes could stop the destruction of their reality by the Twilight God and thus facilitated this outcome. They may have adjusted their game when the adventurers from Vana'diel changed things, blocking access to Shinryu with the Caturae to force the encounters. Then, with the defeat of Shinryu, the Caturariga game was over for Abyssea; the same cannot be said of Vana'diel.
Summary: a group of immortal Zilart live in the Threshold dimension (where Atomos is) and they're bored and like playing games with worlds as the playing field and Caturae and people as the pieces.